3O9I
Crystal Structure of wild-type HIV-1 Protease in complex with af61
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1F7A |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | hanging drop, vapor diffusion | 6.2 | 295 | 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.9 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 50.696 | ¦Á = 90 |
b = 57.505 | ¦Â = 90 |
c = 61.769 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2008-11-07 | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-BM-C | 0.9 | APS | 14-BM-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 1.45 | 50 | 99.8 | 0.047 | 13.8 | 5.1 | 32659 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.45 | 1.5 | 100 | 0.33 | 5.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry ? | 1.45 | 42.11 | 30945 | 1651 | 99.76 | 0.16981 | 0.1688 | 0.18824 | RANDOM | 16.281 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.75 | 0.18 | 0.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.978 |
r_dihedral_angle_4_deg | 11.096 |
r_dihedral_angle_3_deg | 10.635 |
r_dihedral_angle_1_deg | 6.287 |
r_scangle_it | 2.535 |
r_scbond_it | 1.672 |
r_angle_refined_deg | 1.398 |
r_mcangle_it | 1.034 |
r_angle_other_deg | 0.799 |
r_mcbond_it | 0.613 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1494 |
Nucleic Acid Atoms | |
Solvent Atoms | 182 |
Heterogen Atoms | 62 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
AMoRE | phasing |